X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=142023e7a40881c1c6397a761ba350132490b75c;hb=f67ee238c956bb84cfc743b86c41a7e23f1980ba;hp=779ea912ebebbe58ec22e65723899c4ea566b85f;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 779ea91..142023e 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -427,6 +427,11 @@ int GetSeqsCommand::readFasta(){
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 			
 			if (name != "") {
 				//if this name is in the accnos file
@@ -485,13 +490,18 @@ int GetSeqsCommand::readQual(){
 			string name = "";
 			string scores = "";
 			
-			in >> name; 
+			in >> name;
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 				
 			if (name.length() != 0) { 
 				saveName = name.substr(1);
 				while (!in.eof())	{	
 					char c = in.get(); 
-					if (c == 10 || c == 13){	break;	}
+					if (c == 10 || c == 13 || c == -1){	break;	}
 					else { name += c; }	
 				} 
 				m->gobble(in);
@@ -577,7 +587,7 @@ int GetSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
 		
@@ -748,6 +758,8 @@ int GetSeqsCommand::readName(){
 						wroteSomething = true;
 						
 						out << validSecond[0] << '\t';
+                        //we are changing the unique name in the fasta file
+                        uniqueMap[firstCol] = validSecond[0];
 					
 						//you know you have at least one valid second since first column is valid
 						for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
@@ -805,6 +817,7 @@ int GetSeqsCommand::readGroup(){
 
 			in >> name;				//read from first column
 			in >> group;			//read from second column
+            
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {
@@ -862,6 +875,11 @@ int GetSeqsCommand::readTax(){
 
 			in >> name;				//read from first column
 			in >> tax;			//read from second column
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {
@@ -924,6 +942,11 @@ int GetSeqsCommand::readAlign(){
 
 
 			in >> name;				//read from first column
+            
+            if (!dups) {//adjust name if needed
+                map<string, string>::iterator it = uniqueMap.find(name);
+                if (it != uniqueMap.end()) { name = it->second; }
+            }
 			
 			//if this name is in the accnos file
 			if (names.count(name) != 0) {